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It could be wise to tell us the model of your gamepad,
maybe the devs will work for making it compatible with PPSSPP. In the meantime you can use some wrapper library like
this in order to let think the emu that you are using an xobx36 gamepad (although take note that I've not tested this), or use some keyboard simulator like xpadder.
Since English is not my first language sorry for some misspelling on my posts
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It depends on which ppsspp version you use.
The versions on which Option=>Controls work you don't need to do anything
On version Options=>Controls don't work,you have to go to(screen menus)System=>Controls=>left to page 3(Pad) and enable "mapping active"
If it doesn't work,go to Control Panel=>Game Controllers=>Advanced=>make sure the controller is selected
Using PPSSPP on Windows 7 x64 SP1
i7 4771 3.5Ghz,GTX750TI,16GB RAM
Batch iso <=> cso converter
http://forums.ppsspp.org/showthread.php?tid=5384
Save Game\States Manager
http://forums.ppsspp.org/showthread.php?tid=5516